Title :

Vers des sequences parfaites: correction de donnée de sequencage de seconde generation via alignement sur graphe de De Bruijn

Author(s) :

Limasset, Antoine [Auteur correspondant]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Flot, Jean-François [Auteur]
Evolutionary Biology and Ecology [Brussels]
Peterlongo, Pierre [Auteur]
Scalable, Optimized and Parallel Algorithms for Genomics [GenScale]

Journal title :

Bioinformatics

Publisher :

Oxford University Press (OUP)

Publication date :

2019-02-20

ISSN :

1367-4803

HAL domain(s) :

Informatique [cs]/Bio-informatique [q-bio.QM]

English abstract : [en]

Motivations Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on ...
Show more >Motivations Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large data sets or consider reads as mere suites of k-mers, without taking into account their full-length read information. Results We propose a new method to correct short reads using de Bruijn graphs, and implement it as a tool called Bcool. As a first step, Bcool constructs a compacted de Bruijn graph from the reads. This graph is filtered on the basis of k-mer abundance then of unitig abundance, thereby removing from most sequencing errors. The cleaned graph is then used as a reference on which the reads are mapped to correct them. We show that this approach yields more accurate reads than k-mer-spectrum correctors while being scalable to human-size genomic datasets and beyond. Availability and ImplementationShow less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

ANR Project :

Metagenomique comparative comme instrument de mesure pour la biodiversité. Application à l'étude de la vie dans les océans

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL